write_labeling_to_files

besca.export.write_labeling_to_files(adata: AnnData, outpath: Optional[str] = None, column: str = 'leiden', label: str = 'LABEL', filename: str = 'cell2labels.tsv', export_average: bool = True, export_fractpos: bool = True, use_raw: bool = True) → None[source]

export mapping of cells to specified label to .tsv file

This is a function with which any type of labeling (i.e. celltype annotation, leiden clustering, etc.) can be written out to a .tsv file. The generated file can then also be easily uploaded to the database since it fullfilles the FAIR document standards.

To ensure FAIR compatbility label, and file name should not be changed.

Parameters:

  • adata (AnnData) – the AnnData object containing the label

  • directory (outpath str | default = current working) – filepath to the directory in which the results should be outputed, if no directory is specified it outputs the results to the current working directory.

  • column (str | default = ‘leiden’) – Name of the column in adata.obs that is to be mapped to cell barcodes and written out to file.

  • label (str | default = ‘LABEL’) – label above the column when it is written out to file

  • filename (str | default = ‘cell2labels.tsv’) – Filename that is written out.

Returns:

files are written out.

Return type:

None